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3nrf

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of an ApaG protein (PA1934) from PSEUDOMONAS AERUGINOSA at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3nrf Target Id 416839
    Related PDB Ids 3sb3 
    Molecular Characteristics
    Source Pseudomonas aeruginosa pao1
    Alias Ids TPS33852,NP_250624.1, 327491 Molecular Weight 11077.76 Da.
    Residues 105 Isoelectric Point 5.30
    Sequence aapdavmvfarqgdkgsvsvgdkhfrtqafkvrlvnaakseislknsclvaqsaagqsfrldtvdeelt adtlkpgasvegdaifaseddavygaslvrlsdrck
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.50 Rfree 0.222
    Matthews' coefficent 2.31 Rfactor 0.184
    Waters 215 Solvent Content 46.70

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3nrf
    1. Assessment of protein structure refinement in CASP9
    JL MacCallum, A Prez, MJ Schnieders - Proteins: Structure, , 2011 - Wiley Online Library
     
    2. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

    Pfam Update

    There was a hit to TRF2 (PF11611) below threshold, and this was found on building a family from the sequence. One other member has a structure,(3cfu) which is distantly related to 1lmi and 3nrf indicating that the sequence might be an immuno-protective extracellular protein, falling into the Ig-fold SCOP-fold level. I have built it as DUF4354, PF14263. Co-incidentally, I have renamed the TRF2 family as DUF4352, as the annotation relating to telomeres was clearly incorrect. You might want to alter the TOPSAN info for 3nrf and 3cfu in relation to PF11611.

     

    The structure was determined by three wavelength Se-MAD phasing at a resolution of 1.5 Angstroms. Assignment to this family is confirmed by a significant structural similarity to only other solved structure from this family (3cfu - yjhA protein from Bacillus subtilis solved by NESG).  A ribbon representation of the monomer of target PA1934 is shown below. The ribbons are color-coded with the N-terminal end in blue and the C-terminal end in red.

     

    monomer.png

     

     

     The structure described here shows similarity to those in the ApaG-like Superfamily and can be classified as showing an  immunoglobin-like beta-sandwich SCOP fold. Crystal packing suggests that a tetramer is a significant oligomerization state. Shown below is a ribbons representation of a tetramer.

     

    tetramer.png

     

     

     

     

    A disulfide bond linking Cys 125 at the C-terminal end of the monomer, and Cys 69, was observed in the structure. Shown below is a representation of this disulfide linkage with 2fo-fc electron density contoured at 2 sigma shown in pink.

     

    disulfide.bmp

     

     

     

     

     

     

     

     

     

     

    DALI Hits

    PDB ID
    DALI Z-Score
    rmsd overlap (Angstrom)
    length of alignment
    number residues in target
    % sequence ID
    Descriptrion
    1lmi 6.2 2.9 88 131 14 Secreted Protein from Mycobacterium tuberculosis MPT-63
    3cfu 5.9 3.1 90 145 16 yjhA protein from Bacillus subtilis, Northeast Structural Genomics Consortium target SR562
    2vl4 5.5 3.8 80 836 1 Structural and Biochemical Evidence for a Boat-like transition state in beta-mannosidases.
    1tza 5.4 3.8 89 132 11 Northeast Strictural Genomics Consortium Target Sor45
    3cmg 5.4 3.3 81 661 15 Putative beta-galactosidase from Bacteroides fragilis
    1xq4 5.3 3.9 85 122 14 Putative ApaA Protein from Bordetella pertissis. Northeast Structural Genomics Target BeR40

    Ligand Summary

    Reviews

    References

     

    No references found.

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